SNP callers like Lo-Freq are meant for mixed populations. We used it when developing PELE-Seq (paired-end low error sequencing) which is a wet lab approach to detecting low frequency mutations. We examined cancer mitochondrial genotypes and were able to detect sub-population heteroplasmy. You could detect heteroplasmy with just Lo-Freq, but would need to discard SNPs below ~1-5% depending on the read depth and quality.

SNP callers like Lo-Freq are meant for mixed populations. We used it when developing PELE-Seq (paired-end low error sequencing) which is a wet lab approach to detecting low frequency mutations. We examined cancer mitochondrial genotypes and were able to detect sub-population heteroplasmy. You could detect heteroplasmy with just Lo-Freq, but would need to discard SNPs below ~1-5% depending on the read depth and quality.

Thanks for your nice method recommendation. Another problem would be how to measure the heteroplasmy level of mitochondrial DNA. Thanks!